Structure of PDB 4pmt Chain A Binding Site BS01

Receptor Information
>4pmt Chain A (length=273) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CVHHIKRRDIVLKWELGEGAFGKVFLAECHNLDKMLVAVKALDFQREAEL
LTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAG
GEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLV
VKIGDFSRDIYSTDYYRVTMLPIRWMPPESILYRKFTTESDVWSFGVVLW
EIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREP
QQRHSIKDVHARLQALAQAHHHH
Ligand information
Ligand ID31Y
InChIInChI=1S/C23H23N7O/c1-2-17(14-24-9-1)15-25-21-8-7-20-22(29-21)23(27-16-26-20)28-18-3-5-19(6-4-18)30-10-12-31-13-11-30/h1-9,14,16H,10-13,15H2,(H,25,29)(H,26,27,28)
InChIKeyDCLOYUQZPOKYDM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1cc(cnc1)CNc2ccc3c(n2)c(ncn3)Nc4ccc(cc4)N5CCOCC5
CACTVS 3.385C1CN(CCO1)c2ccc(Nc3ncnc4ccc(NCc5cccnc5)nc34)cc2
ACDLabs 12.01n1cccc(c1)CNc5nc2c(ncnc2Nc4ccc(N3CCOCC3)cc4)cc5
FormulaC23 H23 N7 O
NameN~4~-[4-(morpholin-4-yl)phenyl]-N~6~-(pyridin-3-ylmethyl)pyrido[3,2-d]pyrimidine-4,6-diamine
ChEMBLCHEMBL3298264
DrugBank
ZINCZINC000098208380
PDB chain4pmt Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4pmt Maximizing diversity from a kinase screen: identification of novel and selective pan-Trk inhibitors for chronic pain.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		L516 G517 A542 F589 M592 R599 L657 R673
Binding residue
(residue number reindexed from 1)		L16 G17 A38 F76 M79 R86 L144 R158
Annotation score1
Binding affinityMOAD: ic50=997nM
PDBbind-CN: -logKd/Ki=6.00,IC50=997nM
BindingDB: IC50=997nM
Enzymatic activity
Catalytic site (original residue number in PDB) D650 A652 R654 N655 D668 S677 L689
Catalytic site (residue number reindexed from 1) D137 A139 R141 N142 D155 S162 L171
Enzyme Commision number 2.7.10.1: receptor protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0004714 transmembrane receptor protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation
GO:0007169 cell surface receptor protein tyrosine kinase signaling pathway
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4pmt, PDBe:4pmt, PDBj:4pmt
PDBsum4pmt
PubMed24914455
UniProtP04629|NTRK1_HUMAN High affinity nerve growth factor receptor (Gene Name=NTRK1)

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